Mouse 1.3 - Githubissues

SysBioChalmers / Mouse-GEM

Genome-scale model for Mus musculus

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Mouse 1.3 #14

Closed haowang-bioinfo closed 2 years ago

haowang-bioinfo commented 2 years ago

Main improvements in this PR:

Fixes (PR 382):
- resolves issues reported in #11, #12, #13
Fixes (commit 88826a8e5b67669e1c2888500e885035a782b04b):
- change compartment abbreviation from p to x, to sync with changes made in Human-GEM PR 341
Features (commit f74fd2beece82ddc4137e342b6749156bebccd23):
- update ortholog pairs from Alliance of Genomes to ver 5.1.0
Style (PR #9):
- add .gitattributes to ensure consistent LF (\n) line endings
- add citation
- rename branches: master --> main, devel --> develop

haowang-bioinfo commented 2 years ago

would be nice to mention in the Readme or the release text what version of Human-GEM this is based. Also, there is an update of orthologs, perhaps the reason behind that should also be stated.

Good point, will include this info to the release message

JonathanRob commented 2 years ago

Very nice, @haowang-bioinfo!

I don't think I've ever seen this before though:

haowang-bioinfo commented 2 years ago

I don't think I've ever seen this before though

this is probably due to the huge raw data of ortholog pairs downloaded from Alliance of Genomes, any thoughts in avoiding this?

JonathanRob commented 2 years ago

I think it's ok - it almost seems like a bug; only 8 files changed. The 8... fell over... or something.

haowang-bioinfo commented 2 years ago

I think it's ok - it almost seems like a bug

Instead of updating the huge raw data of ortholog pairs, a more decent way might be just logging the extracted pairs in tsv format

To release new Mouse-GEM with all the changes, a new Human-GEM release probably should also be pushed?

mihai-sysbio commented 2 years ago

Instead of updating the huge raw data of ortholog pairs, a more decent way might be just logging the extracted pairs in tsv format

Very good idea!

To release new Mouse-GEM with all the changes, a new Human-GEM release probably should also be pushed?

Another option is to link either the Human-GEM PR that was used, or the merge commit hash https://github.com/SysBioChalmers/Human-GEM/commit/ff109f2283e06bc741ccd991c87ecc11a87a17a6 .

haowang-bioinfo commented 2 years ago

merge commit hash https://github.com/SysBioChalmers/Human-GEM/commit/ff109f2283e06bc741ccd991c87ecc11a87a17a6 .

this is an easier option